track.shift: Tracking back shifts (speciation or extinction) on TreeSimGM simulated tree

Description

track.shift returns all changes in speciation or extinction between the root of a tree and a specific node or tip in a phylogenetic tree simulated with TreeSimGM. It can track back changes on the speciation process (shift='sp') or on the extinction process (shift='ext'). Changes are the multipliers of the drawn waiting times.

Usage

track.shift(shift="sp",tree, node)

Arguments

shift

specifies which macroevolutionary process shall be tracked. Can be "sp" or "ext" for tracking speciation or extinction shifts repectively (default is "sp").

tree

is the simulated tree object.

node

is the node number or tip label that should be tracked. The numbers are the number of the attributes tip.label or as specified in '$edge' on the phylo tree object.

Value

out

is a vector of changes, i.e. scaling factors of the waiting times process, from MRCA until the desired node. Each reported scaling factor is named with a node number (as in $edge). The scaling factor change happened at the start of the branch ancestral to that named node.

References

O. Hagen and T. Stadler (2017). TreeSimGM: Simulating phylogenetic trees under general Bellman Harris models with lineage-specific shifts of speciation and extinction in R. Methods in Ecology and Evolution.

O. Hagen, K. Hartmann, M. Steel and T. Stadler (2015). Age-dependent Speciation can Explain the Shape of Empirical Trees. Systematic Biology. 64, v.3, p.432-440.

Examples

Run this code

# NOT RUN {
# setting seed for reproductibility

set.seed(2142) 

# Simulating a tree under an asymmetric speciation mode with frequent changes in 
# speciation and extinction (repectively 50% and 30% probability)

shif_spext_asym <- sim.taxa(numbsim=1, n=5,  waitsp="rexp(1)", 
waitext="rexp(0.5)", symmetric = FALSE, 
shiftsp=list(prob=0.5, strength="rnorm(0.5,0.01)"), 
shiftext=list(prob=0.3, strength="runif(0,0.5)"))

# visualiying the generated stochastic tree

plot(shif_spext_asym[[1]]) 


# tracking speciation shifts for species 3
# note that this function returns the shifts on the branches
# starting from the mrca

track.shift(shift="sp", tree=shif_spext_asym[[1]], node=3)

# tracking speciation shifts for species 7

track.shift(shift="sp", tree=shif_spext_asym[[1]], node=7)

# tracking extinction shifts for species 7

track.shift(shift="ext", tree=shif_spext_asym[[1]], node=7)
# }